The dominant specialised cropping system (SCS) has supported the increasing population in China, although this agricultural production paradigm could lead to environmental problems. The modern integrated crop-livestock system (ICLS) in China, designed as a recycling paradigm, can alleviate the negative environmental impacts of SCS. However, it must be better investigated, especially due to the trade-off between increased production and environmental harm. In this study, we set up a multi-criteria evaluation with eight indicators based on emergy analysis to quantify and compare the performance of ICLS and SCS and to evaluate the performance of the indicators along a gradient when a proportion of chemical nitrogen is substituted with manure fertiliser nitrogen (PCSM). We examined one experimental modern ICLS and an average SCS by conducting a household survey in Shandong province. The results showed that the ICLS puts less pressure on the environment (ELR = 1.04), has higher emergy sustainability (ESI = 1.09), and generates higher economic benefits per unit area of land (LPO = 3789.94 $-ha(-1)). However, the productivity of the ICLS is lower (Tr = 1.66E+05 sej-J-1, EOD = 1.07E+11 Jha(-1)-yr(-1), EYR = 1.13) than that of the SCS. With an increasing gradient of PCSM, for both systems, the productivity and environmental pressure decreased sharply; this trade-off was less marked for the ICLS. Considering sustainable resource utilisation, environmentally friendly production, and system stability, the ICLS could be an option for Chinese agricultural production in regions with serious issues of manure pollution and cultivated land degradation. However, the ICLS needs to optimise the crop-livestock structure, strengthen scientific management, and improve productivity.